port matching the intake manifold?

You probably won't see any HP/torque difference with an intake manifold port that is slighty smaller (3mm) than the intake runner on the head side. Now if it was the other way around, you would have flow turbulence and lose HP/torque. If you do make the ports line-up perfectly, it will only be "eye-wash", unless you enlarge the port runner all the way up to the plenum. I'd leave such a small step alone.